Have to make a retraction. The golden thing going into Neo's chest definitely isn't Smith. If you look closely at the trailer, you see a sentinel crash through the window of their ship and then it cuts to the shot of something crashing into Neo. You can clearly see the tentacles of the sentinel if you look closely enough. That certainly supports the idea that the "real" world is simply another sort of matrix, though. And it doesn't negate the possibility that Neo and Smith do eventually combine somehow. It just isn't in that scene.